Plant Secondary Metabolites as Defenses, Regulators, and Primary Metabolites: The Blurred Functional Trichotomy

DNA methylation regulates biosynthesis of tanshinones and phenolic acids during growth of Salvia miltiorrhiza

DNA methylation plays a crucial role in the regulation of plant growth and the biosynthesis of secondary metabolites. Danshen (Salvia miltiorrhiza) is a valuable Chinese herbal medicine commonly used to treat cardiovascular diseases; its active ingredients are tanshinones and phenolic acids, which primarily accumulate in roots. Here, we conducted a targeted metabolic analysis of S. miltiorrhiza roots at 3 distinct growth stages: 40 d old (r40), 60 d old (r60), and 90 d old (r90). The contents of tanshinones (cryptotanshinone, tanshinone I, tanshinone IIA, and rosmariquinone) and phenolic acids (rosmarinic acid and salvianolic acid B) gradually increased during plant development. Whole-genome bisulfite sequencing and transcriptome sequencing of roots at the 3 growth stages revealed an increased level of DNA methylation in the CHH context (H represents A, T, or C) context at r90 compared with r40 and r60. Increased DNA methylation levels were associated with elevated expression of various genes linked to epigenetic regulations, including CHROMOMETHYLASE2 (SmCMT2), Decrease in DNA Methylation 1 (SmDDM1), Argonaute 4 (SmAGO4), and DOMAINS REARRANGED METHYLTRANSFERASE 1 (SmDRM1). Moreover, expression levels of many genes involved in tanshinone and salvianolic acid biosynthesis, such as copalyldiphosphate synthase 5 (SmCPS5), cytochrome P450-related enzyme (SmCYP71D464), geranylgeranyl diphosphate synthase (SmGGPPS1), geranyl diphosphate synthase (SmGPPS), hydroxyphenylpyruvate reductase (SmHPPR), and hydroxyphenylpyruvate dioxygenase (SmHPPD), were altered owing to hyper-methylation, indicating that DNA methylation plays an important role in regulating tanshinone and phenolic acid accumulation. Our data shed light on the epigenetic regulation of root growth and the biosynthesis of active ingredients in S. miltiorrhiza, providing crucial clues for further improvement of active compound production via molecular breeding in S. miltiorrhiza.

Universal signatures of transposable element compartmentalization across eukaryotic genomes

The evolutionary mechanisms that drive the emergence of genome architecture remain poorly understood but can now be assessed with unprecedented power due to the massive accumulation of genome assemblies spanning phylogenetic diversity1,2. Transposable elements (TEs) are a rich source of large-effect mutations since they directly and indirectly drive genomic structural variation and changes in gene expression3. Here, we demonstrate universal patterns of TE compartmentalization across eukaryotic genomes spanning ~1.7 billion years of evolution, in which TEs colocalize with gene families under strong predicted selective pressure for dynamic evolution and involved in specific functions. For non-pathogenic species these genes represent families involved in defense, sensory perception and environmental interaction, whereas for pathogenic species, TE-compartmentalized genes are highly enriched for pathogenic functions. Many TE-compartmentalized gene families display signatures of positive selection at the molecular level. Furthermore, TE-compartmentalized genes exhibit an excess of high-frequency alleles for polymorphic TE insertions in fruit fly populations. We postulate that these patterns reflect selection for adaptive TE insertions as well as TE-associated structural variants. This process may drive the emergence of a shared TE-compartmentalized genome architecture across diverse eukaryotic lineages.

Root-exuded specialized metabolites reduce arsenic toxicity in maize

By releasing specialized metabolites, plants modify their environment. Whether and how specialized metabolites protect plants against toxic levels of trace elements is not well understood. We evaluated whether benzoxazinoids, which are released into the soil by major cereals, can confer protection against arsenic toxicity. Benzoxazinoid-producing maize plants performed better in arsenic-contaminated soils than benzoxazinoid-deficient mutants in the greenhouse and the field. Adding benzoxazinoids to the soil restored the protective effect, and the effect persisted to the next crop generation via positive plant-soil feedback. Arsenate levels in the soil and total arsenic levels in the roots were lower in the presence of benzoxazinoids. Thus, the protective effect of benzoxazinoids is likely soil-mediated and includes changes in soil arsenic speciation and root accumulation. We conclude that exuded specialized metabolites can enhance protection against toxic trace elements via soil-mediated processes and may thereby stabilize crop productivity in polluted agroecosystems.

Simultaneous Impact of Rhizobacteria Inoculation and Leaf-Chewing Insect Herbivory on Essential Oil Production and VOC Emissions in Ocimum basilicum

Inoculation with rhizobacteria and feeding by herbivores, two types of abiotic stress, have been shown to increase the production of secondary metabolites in plants as part of the defense response. This study explored the simultaneous effects of inoculation with Bacillus amyloliquefaciens GB03 (a PGPR species) and herbivory by third-instar Spodoptera frugiperda larvae on essential oil (EO) yield and volatile organic compound (VOC) emissions in Ocimum basilicum plants. The density of glandular trichomes was also examined, given that they are linked to EO production and VOC emission. Herbivory increased EO content, but inoculation on its own did not. When combined, however, the two treatments led to a 10-fold rise in EO content with respect to non-inoculated plants. VOC emissions did not significantly differ between inoculated and non-inoculated plants, but they doubled in plants chewed by the larvae with respect to their undamaged counterparts. Interestingly, no changes were observed in VOC emissions when the treatments were tested together. In short, the two biotic stressors elicited differing plant defense responses, mainly when EO was concerned. PGPR did not stimulate EO production, while herbivory significantly enhanced it and increased VOC emissions. The combined treatment acted synergistically, and in this case, PGPR inoculation may have had a priming effect that amplified plant response to herbivory. Peltate trichome density was higher in inoculated plants, those damaged by larvae, and those subjected to the combination of both treatments. The findings highlight the intricate nature of plant defense mechanisms against various stressors and hint at a potential strategy to produce essential oil through the combined application of the two stressors tested here.

Novel loci associated with resistance to downy and powdery mildew in grapevine

Among the main challenges in current viticulture, there is the increasing demand for sustainability in the protection from fungal diseases, such as downy mildew (DM) and powdery mildew (PM). Breeding disease-resistant grapevine varieties is a key strategy for better managing fungicide inputs. This study explores the diversity of grapevine germplasm (cultivated and wild) from Caucasus and neighboring areas to identify genotypes resistant to DM and PM, based on 13 Simple Sequence Repeat (SSR) loci and phenotypical (artificial pathogen inoculation) analysis, and to identify loci associated with DM and PM resistance, via Genome-Wide Association Analysis (GWAS) on Single Nucleotide Polymorphism (SNP) profiles. SSR analysis revealed resistant alleles for 16 out of 88 genotypes. Phenotypic data identified seven DM and 31 PM resistant genotypes. GWAS identified two new loci associated with DM resistance, located on chromosome 15 and 16 (designated as Rpv36 and Rpv37), and two with PM resistance, located on chromosome 6 and 17 (designated as Ren14 and Ren15). The four novel loci identified genomic regions rich in genes related to biotic stress response, such as genes involved in pathogen recognition, signal transduction and resistance response. This study highlights potential candidate genes associated with resistance to DM and PM, providing valuable insights for breeding programs for resistant varieties. To optimize their utilization, further functional characterization studies are recommended.

Enhancing the quality of fermented plant leaves: the role of metabolite signatures and associated fungi

Fungi play a pivotal role in fermentation processes, influencing the breakdown and transformation of metabolites. However, studies focusing on the effects of fungal-metabolite correlations on leaf fermentation quality enhancement are limited. This study investigated specific metabolites and fungi associated with high- and low-quality fermented plant leaves. Their changes were monitored over fermentation periods of 0, 8, 16, and 24 days. The results indicated that organoheterocyclic compounds, lipids, lipid-like molecules, organic nitrogen compounds, phenylpropanoids, and polyketides were predominant in high-quality samples. The fungi Saccharomyces (14.8%) and Thermoascus (4.6%) were predominantly found in these samples. These markers exhibited significant changes during the 24-day fermentation period. The critical influence of fungal community equilibrium was demonstrated by interspecies interactions (e.g., between Saccharomyces and Eurotium). A co-occurrence network analysis identified Saccharomyces as the primary contributor to high-quality samples. These markers collectively enhance the quality and sensory characteristics of the final product.

Comprehensive analysis of MAPK gene family in upland cotton (Gossypium hirsutum) and functional characterization of GhMPK31 in regulating defense response to insect infestation

KEY MESSAGE

The transcriptomic, phenotypic and metabolomic analysis of transgenic plants overexpressing GhMPK31 in upland cotton revealed the regulation of H2O2 burst and the synthesis of defensive metabolites by GhMPK31. Mitogen-activated protein kinases (MAPKs) are a crucial class of protein kinases, which play an essential role in various biological processes in plants. Upland cotton (G. hirsutum) is the most widely cultivated cotton species with high economic value. To gain a better understanding of the role of the MAPK gene family, we conducted a comprehensive analysis of the MAPK gene family in cotton. In this study, a total of 55 GhMPK genes were identified from the whole genome of G. hirsutum. Through an investigation of the expression patterns under diverse stress conditions, we discovered that the majority of GhMPK family members demonstrated robust responses to abiotic stress, pathogen stress and pest stress. Furthermore, the overexpression of GhMPK31 in cotton leaves led to a hypersensitive response (HR)-like cell death phenotype and impaired the defense capability of cotton against herbivorous insects. Transcriptome and metabolomics data analysis showed that overexpression of GhMPK31 enhanced the expression of H2O2-related genes and reduced the accumulation of defensive related metabolites. The direct evidence of GhMPK31 interacting with GhRBOHB (H2O2-generating protein) were found by Y2H, BiFC, and LCI. Therefore, we propose that the increase of H2O2 content caused by overexpression of GhMPK31 resulted in HR-like cell death in cotton leaves while reducing the accumulation of defensive metabolites, ultimately leading to a decrease in the defense ability of cotton against herbivorous insects. This study provides valuable insights into the function of MAPK genes in plant resistance to herbivorous insects.

Integrated metabolome and transcriptome analyses reveal the molecular mechanism underlying dynamic metabolic processes during taproot development of Panax notoginseng

BACKGROUND

Panax notoginseng (Burk) F. H. Chen is one of the most famous Chinese traditional medicinal plants. The taproot is the main organ producing triterpenoid saponins, and its development is directly linked to the quality and yield of the harvested P. notoginseng. However, the mechanisms underlying the dynamic metabolic changes occurring during taproot development of P. notoginseng are unknown.

RESULTS

We carried out metabolomic and transcriptomic analyses to investigate metabolites and gene expression during the development of P. notoginseng taproots. The differentially accumulated metabolites included amino acids and derivatives, nucleotides and derivatives, and lipids in 1-year-old taproots, flavonoids and terpenoids in 2- and 3-year-old taproots, and phenolic acids in 3-year-old taproots. The differentially expressed genes (DEGs) are related to phenylpropanoid biosynthesis, metabolic pathway and biosynthesis of secondary metabolites at all three developmental stages. Integrative analysis revealed that the phenylpropanoid biosynthesis pathway was involved in not only the development of but also metabolic changes in P. notoginseng taproots. Moreover, significant accumulation of triterpenoid saponins in 2- and 3-year-old taproots was highly correlated with the up-regulated expression of cytochrome P450s and uridine diphosphate-dependent glycosyltransferases genes. Additionally, a gene encoding RNase-like major storage protein was identified to play a dual role in the development of P. notoginseng taproots and their triterpenoid saponins synthesis.

CONCLUSIONS

These results elucidate the molecular mechanism underlying the accumulation of and change relationship between primary and secondary metabolites in P. notoginseng taproots, and provide a basis for the quality control and genetic improvement of P. notoginseng.

Multi-omics analysis reveals the biosynthesis of flavonoids during the browning process of Malus sieversii explants

Malus sieversii is a precious apple germplasm resource. Browning of explants is one of the most important factors limiting the survival rate of plant tissue culture. In order to explore the molecular mechanism of the browning degree of different strains of Malus sieversii, we compared the dynamic changes of Malus sieversii and Malus robusta Rehd. during the whole browning process using a multi-group method. A total of 44 048 differentially expressed genes (DEGs) were identified by transcriptome analysis on the DNBSEQ-T7 sequencing platform. KEGG enrichment analysis showed that the DEGs were significantly enriched in the flavonoid biosynthesis pathway. In addition, metabonomic analysis showed that (-)-epicatechin, astragalin, chrysin, irigenin, isoquercitrin, naringenin, neobavaisoflavone and prunin exhibited different degrees of free radical scavenging ability in the tissue culture browning process, and their accumulation in different varieties led to differences in the browning degree among varieties. Comprehensive transcriptome and metabonomics analysis of the data related to flavonoid biosynthesis showed that PAL, 4CL, F3H, CYP73A, CHS, CHI, ANS, DFR and PGT1 were the key genes for flavonoid accumulation during browning. In addition, WGCNA analysis revealed a strong correlation between the known flavonoid structure genes and the selected transcriptional genes. Protein interaction predictions demonstrated that 19 transcription factors (7 MYBs and 12 bHLHs) and 8 flavonoid structural genes had targeted relationships. The results show that the interspecific differential expression of flavonoid genes is the key influencing factor of the difference in browning degree between Malus sieversii and Malus robusta Rehd., providing a theoretical basis for further study on the regulation of flavonoid biosynthesis.

Molecular mechanism of miRNA mediated biosynthesis of secondary metabolites in medicinal plants

Plant secondary metabolites are important raw materials for the pharmaceutical industry, and their biosynthetic processes are subject to diverse and precise regulation by miRNA. The identification of miRNA molecules in medicinal plants and exploration of their mechanisms not only contribute to a deeper understanding of the molecular genetic mechanisms of plant growth, development and resistance to stress, but also provide a theoretical basis for elucidating the pharmacological effects of authentic medicinal materials and constructing bioreactors for the synthesis of medicinal secondary metabolite components. This paper summarizes the research reports on the discovery of miRNA in medicinal plants and their regulatory mechanisms on the synthesis of secondary metabolites by searching the relevant literature in public databases. It summarizes the currently discovered miRNA and their functions in medicinal plants, and summarizes the molecular mechanisms regulating the synthesis and degradation of secondary metabolites. Furthermore, it provides a prospect for the research and development of medicinal plant miRNA. The compiled information contributes to a comprehensive understanding of the research progress on miRNA in medicinal plants and provides a reference for the industrial development of related secondary metabolite biosynthesis.

Spatial metabolomics method to reveal differential metabolomes in microregions of Panax quinquefolius roots by using ultra-performance liquid chromatography quadrupole/time of flight-mass spectrometry and desorption electrospray ionization mass spectrometry imaging

Panax quinquefolius is a natural homology medicine and food that is rich in bioactive ingredients, such as ginsenosides and polysaccharides. The combination of ultra-performance liquid chromatography quadrupole/time of flight-mass spectrometry (UPLC-Q-TOF/MS) and desorption electrospray ionization mass spectrometry imaging (DESI-MSI) was used for the first time in a spatial metabolomics analysis to comprehensively evaluate the differential components in different microregions of P. quinquefolius. UPLC-Q-TOF/MS and DESI-MSI combined with principal component analysis and orthogonal partial least squares-discriminant analysis were used to screen differential metabolites. UPLC-Q-TOF/MS and DESI-MSI screened 27 and 23 differential metabolites, respectively, among which 15 differential metabolites were identified by both methods. It was found that some components, such as ginsenoside Rg1 and malonyl-ginsenoside Rc, were mainly distributed in P of the transverse slice of P. quinquefolius roots, while ginsenoside Ro and malonyl-ginsenoside Rd were mainly distributed in C. The methods and results of this study could be used to understand the precise localization, biosynthesis, and biological functions of special metabolites in P. quinquefolius.

Interplay between Amaryllidaceae alkaloids, the bacteriome and phytopathogens in Lycoris radiata

Alkaloids are a large group of plant secondary metabolites with various structures and activities. It is important to understand their functions in the interplay between plants and the beneficial and pathogenic microbiota. Amaryllidaceae alkaloids (AAs) are unique secondary metabolites in Amaryllidaceae plants. Here, we studied the interplay between AAs and the bacteriome in Lycoris radiata, a traditional Chinese medicinal plant containing high amounts of AAs. The relationship between AAs and bacterial composition in different tissues of L. radiata was studied. In vitro experiments revealed that AAs have varying levels of antimicrobial activity against endophytic bacteria and pathogenic fungi, indicating the importance of AA synthesis in maintaining a balance between plants and beneficial/pathogenic microbiota. Using bacterial synthetic communities with different compositions, we observed a positive feedback loop between bacteria insensitive to AAs and their ability to increase accumulation of AAs in L. radiata, especially in leaves. This may allow insensitive bacteria to outcompete sensitive ones for plant resources. Moreover, the accumulation of AAs enhanced by insensitive bacteria could benefit plants when challenged with fungal pathogens. This study highlights the functions of alkaloids in plant-microbe interactions, opening new avenues for designing plant microbiomes that could contribute to sustainable agriculture.

The dosage- and size-dependent effects of micro- and nanoplastics in lettuce roots and leaves at the growth, photosynthetic, and metabolomics levels

The occurrence of microplastics (MPs) and nanoplastics (NPs) in soils potentially induce morphological, physiological, and biochemical alterations in plants. The present study investigated the effects of MPs/NPs on lettuce (Lactuca sativa L. var. capitata) plants by focusing on (i) four different particle sizes of polyethylene micro- and nanoplastics, at (ii) four concentrations. Photosynthetic activity, morphological changes in plants, and metabolomic shifts in roots and leaves were investigated. Our findings revealed that particle size plays a pivotal role in influencing various growth traits of lettuce (biomass, color segmentation, greening index, leaf area, and photosynthetic activity), physiological parameters (including maximum quantum yield - Fv/Fmmax, or quantum yield in the steady-state Fv/FmLss, NPQLss, RfdLss, FtLss, FqLss), and metabolomic signatures. Smaller plastic sizes demonstrated a dose-dependent impact on aboveground plant structures, resulting in an overall elicitation of biosynthetic processes. Conversely, larger plastic size had a major impact on root metabolomics, leading to a negative modulation of biosynthetic processes. Specifically, the biosynthesis of secondary metabolites, phytohormone crosstalk, and the metabolism of lipids and fatty acids were among the most affected processes. In addition, nitrogen-containing compounds accumulated following plastic treatments. Our results highlighted a tight correlation between the qPCR analysis of genes associated with the soil nitrogen cycle (such as NifH, NirK, and NosZ), available nitrogen pools in soil (including NO3- and NH4), N-containing metabolites and morpho-physiological parameters of lettuce plants subjected to MPs/NPs. These findings underscore the intricate relationship between specific plastic contaminations, nitrogen dynamics, and plant performance.

Holistic Approaches to Plant Stress Alleviation: A Comprehensive Review of the Role of Organic Compounds and Beneficial Bacteria in Promoting Growth and Health

Plants select microorganisms from the surrounding bulk soil, which act as a reservoir of microbial diversity and enrich a rhizosphere microbiome that helps in growth and stress alleviation. Plants use organic compounds that are released through root exudates to shape the rhizosphere microbiome. These organic compounds are of various spectrums and technically gear the interplay between plants and the microbial world. Although plants naturally produce organic compounds that influence the microbial world, numerous efforts have been made to boost the efficiency of the microbiome through the addition of organic compounds. Despite further crucial investigations, synergistic effects from organic compounds and beneficial bacteria combinations have been reported. In this review, we examine the relationship between organic compounds and beneficial bacteria in determining plant growth and biotic and abiotic stress alleviation. We investigate the molecular mechanism and biochemical responses of bacteria to organic compounds, and we discuss the plant growth modifications and stress alleviation done with the help of beneficial bacteria. We then exhibit the synergistic effects of both components to highlight future research directions to dwell on how microbial engineering and metagenomic approaches could be utilized to enhance the use of beneficial microbes and organic compounds.

Effects of Root-Root Interactions on the Physiological Characteristics of Haloxylon ammodendron Seedlings

The root traits and response strategies of plants play crucial roles in mediating interactions between plant root systems. Current research on the role of root exudates as underground chemical signals mediating these interactions has focused mainly on crops, with less attention given to desert plants in arid regions. In this study, we focused on the typical desert plant Haloxylon ammodendron and conducted a pot experiment using three root isolation methods (plastic film separation, nylon mesh separation, and no separation). We found that (1) as the degree of isolation increased, plant biomass significantly increased (p < 0.05), while root organic carbon content exhibited the opposite trend; (2) soil electrical conductivity (EC), soil total nitrogen (STN), soil total phosphorus (STP), and soil organic carbon (SOC) were significantly greater in the plastic film and nylon mesh separation treatments than in the no separation treatment (p < 0.05), and the abundance of Proteobacteria and Actinobacteriota was significantly greater in the plastic film separation treatment than in the no separation treatment (p < 0.05); (3) both plastic film and nylon mesh separations increased the secretion of alkaloids derived from tryptophan and phenylalanine in the plant root system compared with that in the no separation treatment; and (4) Pseudomonas, Proteobacteria, sesquiterpenes, triterpenes, and coumarins showed positive correlations, while both pseudomonas and proteobacteria were significantly positively correlated with soil EC, STN, STP, and SOC (p < 0.05). Aurachin D was negatively correlated with Gemmatimonadota and Proteobacteria, and both were significantly correlated with soil pH, EC, STN, STP, and SOC. The present study revealed strong negative interactions between the root systems of H. ammodendron seedlings, in which sesquiterpenoids, triterpenoids, coumarins, and alkaloids released by the roots played an important role in the subterranean competitive relationship. This study provides a deeper understanding of intraspecific interactions in the desert plant H. ammodendron and offers some guidance for future cultivation of this species in the northwestern region of China.

Enhancement of specialized metabolites using CRISPR/Cas gene editing technology in medicinal plants

Plants are the richest source of specialized metabolites. The specialized metabolites offer a variety of physiological benefits and many adaptive evolutionary advantages and frequently linked to plant defense mechanisms. Medicinal plants are a vital source of nutrition and active pharmaceutical agents. The production of valuable specialized metabolites and bioactive compounds has increased with the improvement of transgenic techniques like gene silencing and gene overexpression. These techniques are beneficial for decreasing production costs and increasing nutritional value. Utilizing biotechnological applications to enhance specialized metabolites in medicinal plants needs characterization and identification of genes within an elucidated pathway. The breakthrough and advancement of CRISPR/Cas-based gene editing in improving the production of specific metabolites in medicinal plants have gained significant importance in contemporary times. This article imparts a comprehensive recapitulation of the latest advancements made in the implementation of CRISPR-gene editing techniques for the purpose of augmenting specific metabolites in medicinal plants. We also provide further insights and perspectives for improving metabolic engineering scenarios in medicinal plants.

Natural products as a source of Coronavirus entry inhibitors

The COVID-19 pandemic has had a significant and lasting impact on the world. Four years on, despite the existence of effective vaccines, the continuous emergence of new SARS-CoV-2 variants remains a challenge for long-term immunity. Additionally, there remain few purpose-built antivirals to protect individuals at risk of severe disease in the event of future coronavirus outbreaks. A promising mechanism of action for novel coronavirus antivirals is the inhibition of viral entry. To facilitate entry, the coronavirus spike glycoprotein interacts with angiotensin converting enzyme 2 (ACE2) on respiratory epithelial cells. Blocking this interaction and consequently viral replication may be an effective strategy for treating infection, however further research is needed to better characterize candidate molecules with antiviral activity before progressing to animal studies and clinical trials. In general, antiviral drugs are developed from purely synthetic compounds or synthetic derivatives of natural products such as plant secondary metabolites. While the former is often favored due to the higher specificity afforded by rational drug design, natural products offer several unique advantages that make them worthy of further study including diverse bioactivity and the ability to work synergistically with other drugs. Accordingly, there has recently been a renewed interest in natural product-derived antivirals in the wake of the COVID-19 pandemic. This review provides a summary of recent research into coronavirus entry inhibitors, with a focus on natural compounds derived from plants, honey, and marine sponges.

Integrated metabolomic and transcriptomic dynamic profiles of endopleura coloration during fruit maturation in three walnut cultivars

BACKGROUND

The color of endopleura is a vital factor in determining the economic value and aesthetics appeal of nut. Walnuts (Juglans) are a key source of edible nuts, high in proteins, amino acids, lipids, carbohydrates. Walnut had a variety endopleura color as yellow, red, and purple. However, the regulation of walnut endopleura color remains little known.

RESULTS

To understand the process of coloration in endopleura, we performed the integrative analysis of transcriptomes and metabolomes at two developmental stages of walnut endopleura. We obtained total of 4,950 differentially expressed genes (DEGs) and 794 metabolites from walnut endopleura, which are involved in flavonoid and phenolic biosynthesis pathways. The enrichment analysis revealed that the cinnamic acid, coniferyl alcohol, naringenin, and naringenin-7-O-glucoside were important metabolites in the development process of walnut endopleura. Transcriptome and metabolome analyses revealed that the DEGs and differentially regulated metabolites (DRMs) were significantly enriched in flavonoid biosynthesis and phenolic metabolic pathways. Through co-expression analysis, CHS (chalcone synthase), CHI (chalcone isomerase), CCR (cinnamoyl CoA reductase), CAD (cinnamyl alcohol dehydrogenase), COMT (catechol-Omethyl transferase), and 4CL (4-coumaroyl: CoA-ligase) may be the key genes that potentially regulate walnut endopleura color in flavonoid biosynthesis and phenolic metabolic pathways.

CONCLUSIONS

This study illuminates the metabolic pathways and candidate genes that underlie the endopleura coloration in walnuts, lay the foundation for further study and provides insights into controlling nut's colour.

Exploring the Significance, Extraction, and Characterization of Plant-Derived Secondary Metabolites in Complex Mixtures

Secondary metabolites are essential components for the survival of plants. Secondary metabolites in complex mixtures from plants have been adopted and documented by different traditional medicinal systems worldwide for the treatment of various human diseases. The extraction strategies are the key components for therapeutic development from natural sources. Polarity-dependent solvent-selective extraction, acidic and basic solution-based extraction, and microwave- and ultrasound-assisted extraction are some of the most important strategies for the extraction of natural products from plants. The method needs to be optimized to isolate a specific class of compounds. Therefore, to establish the mechanism of action, the characterization of the secondary metabolites, in a mixture or in their pure forms, is equally important. LC-MS, GC-MS, and extensive NMR spectroscopic strategies are established techniques for the profiling of metabolites in crude extracts. Various protocols for the extraction and characterization of a wide range of classes of compounds have been developed by various research groups and are described in this review. Additionally, the possible means of characterizing the compounds in the mixture and their uniqueness are also discussed. Hyphenated techniques are crucial for profiling because of their ability to analyze a vast range of compounds. In contrast, inherent chemical shifts make NMR an indispensable tool for structure elucidation in complex mixtures.

Unveiling the dynamic relationship of viruses and/or symbiotic bacteria with plant resilience in abiotic stress

In the ecosphere, plants interact with environmental biotic and abiotic partners, where unbalanced interactions can induce unfavourable stress conditions. Abiotic factors (temperature, water, and salt) are primarily required for plants healthy survival, and any change in their availability is reflected as a stress signal. In certain cases, the presence of infectious pathogens such as viruses, bacteria, fungi, protozoa, nematodes, and insects can also create stress conditions in plants, leading to the emergence of disease or deficiency symptoms. While these symptoms are often typical of abiotic or biotic stress, however, there are instances where they can intensify under specific conditions. Here, we primarily summarize the viral interactions with plants during abiotic stress to understand how these associations are linked together during viral pathogenesis. Secondly, focus is given to the beneficial effects of root-associated symbiotic bacteria in fulfilling the basic needs of plants during normal as well as abiotic stress conditions. The modulations of plant functional proteins, and their occurrence/cross-talk, with pathogen (virus) and symbiont (bacteria) molecules are also discussed. Furthermore, we have highlighted the biochemical and systematic adaptations that develop in plants due to bacterial symbiosis to encounter stress hallmarks. Lastly, directions are provided towards exploring potential rhizospheric bacteria to maintain plant-microbes ecosystem and manage abiotic stress in plants to achieve better trait health in the horticulture crops.

Synergistic induction of phytoalexins in Nicotiana attenuata by jasmonate and ethylene signaling mediated by NaWRKY70

Production of the phytoalexins scopoletin and scopolin is regulated by jasmonate (JA) and ethylene signaling in Nicotiana species in response to Alternaria alternata, the necrotrophic fungal pathogen that causes brown spot disease. However, how these two signaling pathways are coordinated to control this process remains unclear. In this study, we found that the levels of these two phytoalexins and transcripts of their key enzyme gene, feruloyl-CoA 6'-hydroxylase 1 (NaF6'H1), were synergistically induced in Nicotiana attenuata by co-treatment with methyl jasmonate (MeJA) and ethephon. By combination of RNA sequencing and virus-induced gene silencing, we identified a WRKY transcription factor, NaWRKY70, which had a similar expression pattern to NaF6'H1 and was responsible for A. alternata-induced NaF6'H1 expression. Further evidence from stable transformed plants with RNA interference, knock out and overexpression of NaWRKY70 demonstrated that it is a key player in the synergistic induction of phytoalexins and plant resistance to A. alternata. Electrophoretic mobility shift, chromatin immunoprecipitation-quantitative PCR, and dual-luciferase assays revealed that NaWRKY70 can bind directly to the NaF6'H1 promoter and activate its expression. Furthermore, the key regulator of the ethylene pathway, NaEIN3-like1, can directly bind to the NaWRKY70 promoter and activate its expression. Meanwhile, NaMYC2s, important JA pathway transcription factors, also indirectly regulate the expression of NaWRKY70 and NaF6'H1 to control scopoletin and scopolin production. Our data reveal that these phytoalexins are synergistically induced by JA and ethylene signaling during A. alternata infection, which is largely mediated by NaWRKY70, thus providing new insights into the defense responses against A. alternata in Nicotiana species.

Flavonoids influence key rhizocompetence traits for early root colonization and PCB degradation potential of Paraburkholderia xenovorans LB400

Introduction

Flavonoids are among the main plant root exudation components, and, in addition to their role in symbiosis, they can broadly affect the functionality of plant-associated microbes: in polluted environments, for instance, flavonoids can induce the expression of the enzymatic degradative machinery to clean-up soils from xenobiotics like polychlorinated biphenyls (PCBs). However, their involvement in root community recruitment and assembly involving non-symbiotic beneficial interactions remains understudied and may be crucial to sustain the holobiont fitness under PCB stress.

Methods

By using a set of model pure flavonoid molecules and a natural blend of root exudates (REs) with altered flavonoid composition produced by Arabidopsis mutant lines affected in flavonoid biosynthesis and abundance (null mutant tt4, flavonoid aglycones hyperproducer tt8, and flavonoid conjugates hyperaccumulator ttg), we investigated flavonoid contribution in stimulating rhizocompetence traits and the catabolic potential of the model bacterial strain for PCB degradation Paraburkholderia xenovorans LB400.

Results

Flavonoids influenced the traits involved in bacterial recruitment in the rhizoplane by improving chemotaxis and motility responses, by increasing biofilm formation and by promoting the growth and activation of the PCB-degradative pathway of strain LB400, being thus potentially exploited as carbon sources, stimulating factors and chemoattractant molecules. Indeed, early rhizoplane colonization was favored in plantlets of the tt8 Arabidopsis mutant and reduced in the ttg line. Bacterial growth was promoted by the REs of mutant lines tt4 and tt8 under control conditions and reduced upon PCB-18 stress, showing no significant differences compared with the WT and ttg, indicating that unidentified plant metabolites could be involved. PCB stress presumably altered the Arabidopsis root exudation profile, although a sudden "cry-for-help" response to recruit strain LB400 was excluded and flavonoids appeared not to be the main determinants. In the in vitro plant-microbe interaction assays, plant growth promotion and PCB resistance promoted by strain LB400 seemed to act through flavonoid-independent mechanisms without altering bacterial colonization efficiency and root adhesion pattern.

Discussions

This study further contributes to elucidate the vast array of functions provided by flavonoids in orchestrating the early events of PCB-degrading strain LB400 recruitment in the rhizosphere and to support the holobiont fitness by stimulating the catabolic machinery involved in xenobiotics decomposition and removal.

Traits linked to natural variation of sulfur content in Arabidopsis thaliana

Sulfur (S) is an essential mineral nutrient for plant growth and development; it is important for primary and specialized plant metabolites that are crucial for biotic and abiotic interactions. Foliar S content varies up to 6-fold under a controlled environment, suggesting an adaptive value under certain natural environmental conditions. However, a major quantitative regulator of S content in Arabidopsis thaliana has not been identified yet, pointing to the existence of either additional genetic factors controlling sulfate/S content or of many minor quantitative regulators. Here, we use overlapping information of two separate ionomics studies to select groups of accessions with low, mid, and high foliar S content. We quantify series of metabolites, including anions (sulfate, phosphate, and nitrate), thiols (cysteine and glutathione), and seven glucosinolates, gene expression of 20 genes, sulfate uptake, and three biotic traits. Our results suggest that S content is tightly connected with sulfate uptake, the concentration of sulfate and phosphate anions, and glucosinolate and glutathione synthesis. Additionally, our results indicate that the growth of pathogenic bacteria is enhanced in the A. thaliana accessions containing higher S in their leaves, suggesting a complex regulation between S homeostasis, primary and secondary metabolism, and biotic pressures.

γ-Aminobutyric acid (GABA) in N2-fixing-legume symbiosis: Metabolic flux and carbon/nitrogen homeostasis in responses to abiotic constraints

Nodule symbiosis is an energetic process that demands a tremendous carbon (C) cost, which massively increases in responses to environmental stresses. Notably, most common respiratory pathways (e.g., glycolysis and Krebs cycle) that sustain nitrogenase activity and subsequent nitrogen (N) assimilation (amino acid formation) display a noncyclic mode of C flux. In such circumstances, the nodule's energy charge could markedly decrease, leading to a lower symbiotic activity under stresses. The host plant then attempts to induce alternative robust metabolic pathways to minimize the C expenditure and compensate for the loss in respiratory substrates. GABA (γ-aminobutyric acid) shunt appears to be among the highly conserved metabolic bypass induced in responses to stresses. Thus, it can be suggested that GABA, via its primary biosynthetic pathway (GABA shunt), is simultaneously induced to circumvent stress-susceptible decarboxylating portion of the Krebs cycle and to replenish symbiosome with energy and C skeletons for enhancing nitrogenase activity and N assimilation besides the additional C costs expended in the metabolic stress acclimations (e.g., biosynthesis of secondary metabolites and excretion of anions). The GABA-mediated C/N balance is strongly associated with interrelated processes, including pH regulation, oxygen (O2) protection, osmoregulation, cellular redox control, and N storage. Furthermore, it has been anticipated that GABA could be implicated in other functions beyond its metabolic role (i.e., signaling and transport). GABA helps plants possess remarkable metabolic plasticity, which might thus assist nodules in attenuating stressful events.

Additive and Specific Effects of Elicitor Treatments on the Metabolic Profile of Arabidopsis thaliana

Several elicitors of plant defense have been identified and numerous efforts to use them in the field have been made. Exogenous elicitor treatments mimic the in planta activation of pattern-triggered immunity (PTI), which relies on the perception of pathogen-associated molecular patterns (PAMPs) such as bacterial flg22 or fungal chitins. Early transcriptional responses to distinct PAMPs are mostly overlapping, regardless of the elicitor being used. However, it remains poorly known if the same patterns are observed for metabolites and proteins produced later during PTI. In addition, little is known about the impact of a combination of elicitors on PTI and the level of induced resistance to pathogens. Here, we monitored Arabidopsis thaliana resistance to the bacterial pathogen Pseudomonas syringae pv. tomato DC3000 (Pto DC3000) following application of flg22 and chitosan elicitors, used individually or in combination. A slight, but not statistically significant increase in induced resistance was observed when the elicitors were applied together when compared with individual treatments. We investigated the effect of these treatments on the metabolome by using an untargeted analysis. We found that the combination of flg22 and chitosan impacted a higher number of metabolites and deregulated specific metabolic pathways compared with the elicitors individually. These results contribute to a better understanding of plant responses to elicitors, which might help better rationalize their use in the field. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Impact of nanopollution on plant growth, photosynthesis, toxicity, and metabolism in the agricultural sector: An updated review

Nanotechnology provides distinct benefits to numerous industrial and commercial fields, and has developed into a discipline of intense interest to researchers. Nanoparticles (NPs) have risen to prominence in modern agriculture due to their use in agrochemicals, nanofertilizers, and nanoremediation. However, their potential negative impacts on soil and water ecosystems, as well as plant growth and physiology, have caused concern for researchers and policymakers. Concerns have been expressed regarding the ecological consequences and toxicity effects associated with nanoparticles as a result of their increased production and usage. Moreover, the accumulation of nanoparticles in the environment poses a risk, not only because of the possibility of plant damage but also because nanoparticles may infiltrate the food chain. In this review, we have documented the beneficial and detrimental effects of NPs on seed germination, shoot and root growth, plant biomass, and nutrient assimilation. Nanoparticles exert toxic effects by inducing ROS generation and stimulating cytotoxic and genotoxic effects, thereby leading to cell death in several plant species. We have provided possible mechanisms by which nanoparticles induce toxicity in plants. In addition to the toxic effects of NPs, we highlighted the importance of nanomaterials in the agricultural sector. Thus, understanding the structure, size, and concentration of nanoparticles that will improve plant growth or induce plant cell death is essential. This updated review reveals the multifaceted connection between nanoparticles, soil and water pollution, and plant biology in the context of agriculture.

Specificity and breadth of plant specialized metabolite-microbe interactions

Plant specialized metabolites shape plant interactions with the environment including plant-microbe interactions. While we often group compounds into generic classes, it is the precise structure of a compound that creates a specific role in plant-microbe or-pathogen interactions. Critically, the structure guides definitive targets in individual interactions, yet single compounds are not limited to singular mechanistic targets allowing them to influence interactions across broad ranges of attackers, from bacteria to fungi to animals. Further, the direction of the effect can be altered by counter evolution within the interacting organism leading to single compounds being both beneficial and detrimental. Thus, the benefit of a single compound to a host needs to be assessed by measuring the net benefit across all interactions while in each specific interaction. Factoring this complexity for single compounds in plant-microbe interactions with the massive expansion in our identification of specialized metabolite pathways means that we need systematic studies to classify the full breadth of activities. Only with this full biological knowledge we can develop mechanistic, ecological, and evolutionary models to understand how plant specialized metabolites fully influence plant-microbe and plant-biotic interactions more broadly.

A study of volatiles of young citrus fruits from four areas based on GC-MS and flash GC e-nose combined with multivariate algorithms

The present study has successfully established a scientific and precise approach for distinguishing the geographical origins of young citrus fruits (Qingpi) from four primary production regions in China, using gas chromatography-mass spectrometry (GC-MS) and flash gas chromatography electronic nose (flash GC e-nose) to analyze the volatile composition and odor characteristics. Through the application of chemometric analysis, a clear differentiation among Qingpi samples was established using GC-MS. Additionally, the application of flash GC e-nose facilitated the extraction of flavor information, which enabled the discrimination of geographical origins. Several flavor components were identified as significant factors for origin certification. Furthermore, two pattern recognition algorithms were employed to achieve high accuracy in regional identification. The results of this investigation demonstrate that the amalgamation of multivariate chemometrics and algorithms can proficiently discern the sources of those young citrus fruits. The findings of this research can provide a reference for the assessment of quality control in food and other agricultural commodities in the times ahead.

Dynamic interplay of metal and metal oxide nanoparticles with plants: Influencing factors, action mechanisms, and assessment of stimulatory and inhibitory effects

Nanoparticles (NPs) of metals and metal oxides have received increasing attention regarding their characteristic behavior in plant systems. The fate and transport of metal NPs and metal oxide NPs in plants is of emerging concern for researchers because they ultimately become part of the food chain. The widespread use of metal-based NPs (MBNPs) in plants has revealed their beneficial and harmful effects. This review addresses the main factors affecting the uptake, translocation, absorption, bioavailability, toxicity, and accumulation of MBNPs in different plant species. It appraises the mechanism of nanoparticle-plant interaction in detail and provides understanding of the estimation strategies for the associated pros and cons with this interplay. Critical parameters of NPs include, but are not limited to, particle size and shape, surface chemistry, surface charge, concentration, solubility, and exposure route. On exposure to MBNPs, the molecular, physiological, and biochemical reactions of plants have been assessed. We have filled knowledge gaps and answered research questions regarding the positive and negative effects of metal and metal oxide NPs on seed germination, callus induction, growth and yield of plant, nutritional content, antioxidants, and enzymes. Besides, the phytotoxicity, cytotoxicity, genotoxicity, and detoxification studies of MBNPs in plants have been outlined. Furthermore, the recent developments and future perspectives of the two-way traffic of interplay of MBNPs and plants have been provided in this comprehensive review.

Chemical Analysis and Biological Activities of Extracts Isolated from Symbiotic L. japonicus Plants

Plants produce a wide variety of secondary metabolites, including compounds with biological activities that could be used for the treatment of human diseases. In the present study, we examined the putative production of bioactive molecules in the legume plant Lotus japonicus, which engages into symbiotic relationships with beneficial soil microorganisms. To monitor the production of secondary metabolites when the plant develops beneficial symbiotic relationships, we performed single and double inoculations with arbuscular mycorrhizal fungi (AMF) and nitrogen-fixing Rhizobium bacteria. Plant extracts from non-inoculated and inoculated plants were chemically characterized and tested for anti-proliferative, apoptotic, and anti-inflammatory effects on human HEK-293 cells. Both shoot and root extracts from non-inoculated and inoculated plants significantly reduced the HEK-293 cell viability; however, a stronger effect was observed when the root extracts were tested. Shoot and root extracts from Rhizobium-inoculated plants and shoot extracts from AMF-inoculated plants showed apoptotic effects on human cells. Moreover, both shoot and root extracts from AMF-inoculated plants significantly reduced TNFα-induced NF-κB transcriptional activity, denoting anti-inflammatory activity. These results suggest that symbiotic L. japonicus plants are enriched with metabolites that have interesting biological activities and could be further explored for putative future use in the pharmaceutical sector.

Recent Advances in the Specialized Metabolites Mediating Resistance to Insect Pests and Pathogens in Tea Plants (Camellia sinensis)

Tea is the second most popular nonalcoholic beverage consumed in the world, made from the buds and young leaves of the tea plants (Camellia sinensis). Tea trees, perennial evergreen plants, contain abundant specialized metabolites and suffer from severe herbivore and pathogen attacks in nature. Thus, there has been considerable attention focusing on investigating the precise function of specialized metabolites in plant resistance against pests and diseases. In this review, firstly, the responses of specialized metabolites (including phytohormones, volatile compounds, flavonoids, caffeine, and L-theanine) to different attacks by pests and pathogens were compared. Secondly, research progress on the defensive functions and action modes of specialized metabolites, along with the intrinsic molecular mechanisms in tea plants, was summarized. Finally, the critical questions about specialized metabolites were proposed for better future research on phytohormone-dependent biosynthesis, the characteristics of defense responses to different stresses, and molecular mechanisms. This review provides an update on the biological functions of specialized metabolites of tea plants in defense against two pests and two pathogens.

Fostering plant growth performance under drought stress using rhizospheric microbes, their gene editing, and biochar

Stress due to drought lowers crop yield and frequently leads to a rise in food scarcity. Plants' intricate metabolic systems enable them to tolerate drought stress, but they are unable to handle it well. Adding some external, environmentally friendly supplements can boost plant growth and productivity when it comes to drought-stressed plants. In order to prevent the detrimental effects of drought in agricultural regions, environmentally friendly practices must be upheld. Plant growth-promoting rhizobacteria (PGPR) can exhibit beneficial phytostimulation, mineralization, and biocontrol activities under drought stress. The significant impact of the PGPR previously reported has not been accepted as an effective treatment to lessen drought stress. Recent studies have successfully shown that manipulating microbes can be a better option to reduce the severity of drought in plants. In this review, we demonstrate how modifying agents such as biochar, PGPR consortia, PGPR, and mycorrhizal fungi can help overcome drought stress responses in crop plants. This article also discusses CRISPR/Cas9-modifiable genes, increase plant's effectiveness in drought conditions, and increase plant resistance to drought stress. With an eco-friendly approach in mind, there is a need for practical management techniques having potential prospects based on an integrated strategy mediated by CRISPR-Cas9 editing, PGPR, which may alleviate the effects of drought stress in crops and aid in achieving the United Nation Sustainable Development Goals (UN-SDGs-2030).

The Effect of External Treatment of Arabidopsis thaliana with Plant-Derived Stilbene Compounds on Plant Resistance to Abiotic Stresses

Stilbenes are a group of plant phenolic secondary metabolites, with trans-resveratrol (3,5,4'-trihydroxy-trans-stilbene) being recognized as the most prominent and studied member. Stilbenes have a great potential for use in agriculture and medicine, as they have significant activities against plant pathogens and have valuable beneficial effects on human health. In this study, we analyzed the effects of direct application of stilbenes, stilbene precursor, and stilbene-rich extract solutions to the plant foliar surface for increasing the resistance of Arabidopsis thaliana to various abiotic stresses (heat, cold, drought, and soil salinity). Exogenous treatment of A. thaliana with stilbenes (trans-resveratrol, piceid, and spruce bark extract) and phenolic precursor (p-coumaric acid or CA) during germination resulted in considerable growth retardation of A. thaliana plants: a strong delay in the root and stem length of 1-week-old seedlings (in 1.3-4.5 fold) and rosette diameter of 1-month-old plants (in 1.2-1.8 fold), while the 2-month-old treated plants were not significantly different in size from the control. Plant treatments with stilbenes and CA increased the resistance of A. thaliana to heat and, to a lesser extent, to soil salinity (only t-resveratrol and spruce extract) to drought (only CA), while cold resistance was not affected. Plant treatments with stilbenes and CA resulted in a significant increase in plant resistance and survival rates under heat, with plants showing 1.5-2.3 times higher survival rates compared to untreated plants. Thus, exogenous stilbenes and a CA are able to improve plant survival under certain abiotic stresses via specific activation of the genes involved in the biosynthesis of auxins, gibberellins, abscisic acid, and some stress-related genes. The present work provides new insights into the application of stilbenes to improve plant stress tolerance.

Effect of 2850 MHz electromagnetic field radiation on the early growth, antioxidant activity, and secondary metabolite profile of red and green cabbage (Brassica oleracea L.)

The proliferation of wireless and other telecommunications equipment brought about by technological advances in the communication industry has substantially increased the radiofrequency radiation levels in the environment. The emphasis is, therefore, placed on investigating the potential impacts of radiofrequency radiation on biota. In this work, the impact of 2850 MHz electromagnetic field radiation (EMF-r) on early development, photosynthetic pigments, and the metabolic profile of two Brassica oleracea L. cultivars (red and green cabbage) was studied. On a daily basis for seven days, seedlings were exposed to homogeneous EMF-r for one, two, and four hours, and observations were carried out at 0-h, 1-h, and 24-h following the final dose. Irrespective of the duration of harvest, exposure to EMF-r resulted in a dose-dependent reduction in both root (from 6.3 cm to 4.0 cm in red; 6.1 cm to 3.8 cm in green) and shoot lengths (from 5.3 cm to ⁓3.1 cm in red; 5.1 cm to 3.1 cm in green), as well as a decrease in biomass (from 2.9 mg to ⁓1.1 mg in red; 2.5 to 0.9 mg in green) of the seedlings when compared to control samples. Likewise, the chlorophyll (from 6.09 to ⁓4.94 mg g-1 d.wt in red; 7.37 to 6.05 mg g-1 d.wt. in green) and carotenoid (from 1.49 to 1.19 mg g-1 d.wt. in red; 1.14 to 0.51 mg g-1 d.wt. in green) contents of both cultivars decreased significantly when compared to the control. Additionally, the contents of phenolic (28.99‒45.52 mg GAE g-1 in red; 25.49‒33.76 mg GAE g-1 in green), flavonoid (21.7‒31.8 mg QE g-1 in red; 12.1‒19.0 mg QE g-1 in green), and anthocyanin (28.8‒43.6 mg per 100 g d.wt. in red; 1.1‒2.6 mg per 100 g d.wt. in green) in both red and green cabbage increased with exposure duration. EMF-r produced oxidative stress in the exposed samples of both cabbage cultivars, as demonstrated by dose-dependent increases in the total antioxidant activity (1.33‒2.58 mM AAE in red; 1.29‒2.22 mM AAE in green), DPPH activity (12.96‒78.33% in red; 9.62‒67.73% in green), H2O2 content (20.0‒77.15 nM g-1 f.wt. in red; 14.28‒64.29 nM g-1 f.wt. in green), and MDA content (0.20‒0.61 nM g-1 f.wt. in red; 0.18‒0.51 nM g-1 f.wt. in green) compared to their control counterparts. The activity of antioxidant enzymes, i.e., superoxide dismutases (3.83‒8.10 EU mg-1 protein in red; 4.19‒7.35 EU mg-1 protein in green), catalases (1.81‒7.44 EU mg-1 protein in red; 1.04‒6.24 EU mg-1 protein in green), and guaiacol peroxidases (14.37‒47.85 EU mg-1 protein in red; 12.30‒42.79 EU mg-1 protein in green), increased significantly compared to their control counterparts. The number of polyphenols in unexposed and EMF-r exposed samples of red cabbage was significantly different. The study concludes that exposure to 2850 MHz EMF-r affects the early development of cabbage seedlings, modifies their photosynthetic pigments, alters polyphenol content, and impairs their oxidative metabolism.

A semiochemical view of the ecology of the seed beetle Acanthoscelides obtectus Say (Coleoptera: Chrysomelidae, Bruchinae)

The dried bean beetle, Acanthoscelides obtectus, is an economically important pest of stored legumes worldwide. Tracking the human-aided dispersion of its primary hosts, the Phaseolus vulgaris beans, it is now widespread in most bean-growing areas of the tropics and subtropics. In temperate regions where it can only occasionally overwinter in the field, A. obtectus proliferates in granaries, having multiple generations a year. Despite its negative impact on food production, no sensitive detection or monitoring tools exist, and the reduction of local populations still relies primarily on inorganic insecticides as fumigating agents. However, in the quest to produce more nutritious food more sustainably and healthily, the development of environmentally benign crop protection methods is vital against A. obtectus. For this, knowledge of the biology and chemistry of both the host plant and its herbivore will underpin the development of, among others, chemical ecology-based approaches to form an essential part of the toolkit of integrated bruchid management. We review the semiochemistry of the mate- and host-finding behaviour of A. obtectus and provide new information about the effect of seed chemistry on the sensory and behavioural ecology of host acceptance and larval development.

Large-scale identification of novel transcriptional regulators of the aliphatic glucosinolate pathway in Arabidopsis

Aliphatic glucosinolates are a large group of plant secondary metabolites characteristic of Brassicaceae, including the model plant Arabidopsis. The diverse and complex degradation products of aliphatic glucosinolates contribute to plant responses to herbivory, pathogen attack, and environmental stresses. Most of the biosynthesis genes in the aliphatic glucosinolate pathway have been cloned in Arabidopsis, and the research focus has recently shifted to the regulatory mechanisms controlling aliphatic glucosinolate accumulation. Up till now, more than 40 transcriptional regulators have been identified as regulating the aliphatic glucosinolate pathway, but many more novel regulators likely remain to be discovered based on research evidence over the past decade. In the current study, we took a systemic approach to functionally test 155 candidate transcription factors in Arabidopsis identified by yeast one-hybrid assay, and successfully validated at least 30 novel regulators that could significantly influence the accumulation of aliphatic glucosinolates in our experimental set-up. We also showed that the regulators of the aliphatic glucosinolate pathway have balanced positive and negative effects, and glucosinolate metabolism and plant development can be coordinated. Our work is the largest scale effort so far to validate transcriptional regulators of a plant secondary metabolism pathway, and provides new insights into how the highly diverse plant secondary metabolism is regulated at the transcriptional level.

Ethylene enhances transcriptions of asparagine biosynthetic genes in soybean (Glycine max L. Merr) leaves

Soybean, a vital protein-rich crop, offers bioactivity that can mitigate various chronic human diseases. Nonetheless, soybean breeding poses a challenge due to the negative correlation between enhanced protein levels and overall productivity. Our previous studies demonstrated that applying gaseous phytohormone, ethylene, to soybean leaves significantly boosts the accumulation of free amino acids, particularly asparagine (Asn). Current studies also revealed that ethylene application to soybeans significantly enhanced both essential and non-essential amino acid contents in leaves and stems. Asn plays a crucial role in ammonia detoxification and reducing fatigue. However, the molecular evidence supporting this phenomenon remains elusive. This study explores the molecular mechanisms behind enhanced Asn accumulation in ethylene-treated soybean leaves. Transcriptional analysis revealed that ethylene treatments to soybean leaves enhance the transcriptional levels of key genes involved in Asn biosynthesis, such as aspartate aminotransferase (AspAT) and Asn synthetase (ASN), which aligns with our previous observations of elevated Asn levels. These findings shed light on the role of ethylene in upregulating Asn biosynthetic genes, subsequently enhancing Asn concentrations. This molecular insight into amino acid metabolism regulation provides valuable knowledge for the metabolic farming of crops, especially in elevating nutraceutical ingredients with non-genetic modification (GM) approach for improved protein content.

Subcellular compartmentalization in the biosynthesis and engineering of plant natural products

Plant natural products (PNPs) are specialized metabolites with diverse bioactivities. They are extensively used in the pharmaceutical, cosmeceutical and food industries. PNPs are synthesized in plant cells by enzymes that are distributed in different subcellular compartments with unique microenvironments, such as ions, co-factors and substrates. Plant metabolic engineering is an emerging and promising approach for the sustainable production of PNPs, for which the knowledge of the subcellular compartmentalization of their biosynthesis is instrumental. In this review we describe the state of the art on the role of subcellular compartments in the biosynthesis of major types of PNPs, including terpenoids, phenylpropanoids, alkaloids and glucosinolates, and highlight the efforts to target biosynthetic pathways to subcellular compartments in plants. In addition, we will discuss the challenges and strategies in the field of plant synthetic biology and subcellular engineering. We expect that newly developed methods and tools, together with the knowledge gained from the microbial chassis, will greatly advance plant metabolic engineering.

Metabolome Profiling of Marrubium peregrinum L. and Marrubium friwaldskyanum Boiss Reveals Their Potential as Sources of Plant-Based Pharmaceuticals

Marrubium species have been used since ancient times as food additives and curative treatments. Their phytochemical composition and various pharmacological activities were the focus of a number of scientific investigations but no comprehensive metabolome profiling to identify the numerous primary and secondary metabolites has been performed so far. This study aimed to generate a comprehensive picture of the total metabolite content of two Marrubium species-M. peregrinum and M. friwaldskyanum-to provide detailed information about the main primary and secondary metabolites. In addition, the elemental composition was also evaluated. For this purpose, non-targeted metabolomic analyses were conducted using GC-MS, UPLC-MS/MS and ICP-MS approaches. Nearly 500 compounds and 12 elements were detected and described. The results showed a strong presence of phenolic acids, flavonoids and their glucosides, which are generally of great interest due to their various pharmacological activities. Furthermore, tissue-specific analyses for M. friwaldskyanum stem, leaves and flowers were carried out in order to outline the sources of potentially important bioactive molecules. The results generated from this study depict the Marrubium metabolome and reveal its dual scientific importance-from one side, providing information about the metabolites that is fundamental and vital for the survival of these species, and from the other side, defining the large diversity of secondary substances that are a potential source of phytotherapeutic agents.

Analysis of the effects of sulfamethoxazole on the secondary metabolites and antioxidants in oilseed rape (Brassica napus L.) and the underlying mechanisms

The secondary metabolism of plants is key for mediating responses to environmental stress, but few studies have examined how the relationship between secondary metabolism and the stress response of plants is affected by exposure to antibiotics. Here, we studied the effects of sulfamethoxazole (SMZ) on the secondary metabolism and antioxidant activity of oilseed rape (Brassica napus L.). SMZ significantly affected the growth of rape seedlings. Low and high concentrations of SMZ induced the production of a large number of reactive oxygen species (ROS) in rape seedlings, which damaged cells. SMZ stress altered the activity of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), as well as the content of malondialdehyde (MDA). SMZ promoted the activities of phenylalanine ammonia lyase (PAL), tyrosine ammonia lyase (TAL), cinnamic acid-4-hydroxylase (C4H), and 4-coumaric acid: coenzyme A ligase (4CL) by activating the phenylpropanoid pathway. The content of secondary metabolites changed. The content of phenolic acids and flavonoids increased, and the content of sinapine and anthocyanins was altered to cope with the oxidative damage induced by antibiotics. Transcriptomic and metabolomic analysis showed that differentially expressed genes and differentially expressed metabolites were mainly involved in Phenylpropanoid biosynthesis. SMZ alters the secondary metabolites of rapeseed, which mitigates the deleterious effects of stress, by modulating upstream secondary metabolism pathways and the production of plant hormones involved in signal transduction. In sum, these results provide a new perspective on the effects of SMZ on plants relative to secondary metabolites and improve our understanding of the toxicity of SMZ.

Microbial degradation of plant toxins

Plants produce a variety of secondary metabolites in response to biotic and abiotic stresses. Although they have many functions, a subclass of toxic secondary metabolites mainly serve plants as deterring agents against herbivores, insects, or pathogens. Microorganisms present in divergent ecological niches, such as soil, water, or insect and rumen gut systems have been found capable of detoxifying these metabolites. As a result of detoxification, microbes gain growth nutrients and benefit their herbivory host via detoxifying symbiosis. Here, we review current knowledge on microbial degradation of toxic alkaloids, glucosinolates, terpenes, and polyphenols with an emphasis on the genes and enzymes involved in breakdown pathways. We highlight that the insect-associated microbes might find application in biotechnology and become targets for an alternative microbial pest control strategy.

Metabolomics of early blight (Alternaria solani) susceptible tomato (Solanum lycopersicum) unfolds key biomarker metabolites and involved metabolic pathways

Tomato (Solanum lycopersicum) is among the most important commercial horticultural crops worldwide. The crop quality and production is largely hampered due to the fungal pathogen Alternaria solani causing necrotrophic foliage early blight disease. Crop plants usually respond to the biotic challenges with altered metabolic composition and physiological perturbations. We have deciphered altered metabolite composition, modulated metabolic pathways and identified metabolite biomarkers in A. solani-challenged susceptible tomato variety Kashi Aman using Liquid Chromatography-Mass Spectrometry (LC-MS) based metabolomics. Alteration in the metabolite feature composition of pathogen-challenged (m/z 9405) and non-challenged (m/z 9667) plant leaves including 8487 infection-exclusive and 8742 non-infection exclusive features was observed. Functional annotation revealed putatively annotated metabolites and pathway mapping indicated their enrichment in metabolic pathways, biosynthesis of secondary metabolites, ubiquinone and terpenoid-quinones, brassinosteroids, steroids, terpenoids, phenylpropanoids, carotenoids, oxy/sphingolipids and metabolism of biotin and porphyrin. PCA, multivariate PLS-DA and OPLS-DA analysis showed sample discrimination. Significantly up regulated 481 and down regulated 548 metabolite features were identified based on the fold change (threshold ≥ 2.0). OPLS-DA model based on variable importance in projection (VIP scores) and FC threshold (> 2.0) revealed 41 up regulated discriminant metabolite features annotated as sphingosine, fecosterol, melatonin, serotonin, glucose 6-phosphate, zeatin, dihydrozeatin and zeatin-β-D-glucoside. Similarly, 23 down regulated discriminant metabolites included histidinol, 4-aminobutyraldehyde, propanoate, tyramine and linalool. Melatonin and serotonin in the leaves were the two indoleamines being reported for the first time in tomato in response to the early blight pathogen. Receiver operating characteristic (ROC)-based biomarker analysis identified apigenin-7-glucoside, uridine, adenosyl-homocysteine, cGMP, tyrosine, pantothenic acid, riboflavin (as up regulated) and adenosine, homocyctine and azmaline (as down regulated) biomarkers. These results could aid in the development of metabolite-quantitative trait loci (mQTL). Furthermore, stress-induced biosynthetic pathways may be the potential targets for modifications through breeding programs or genetic engineering for improving crop performance in the fields.

Enhancement of Growth and Secondary Metabolites by the Combined Treatment of Trace Elements and Hydrogen Water in Wheat Sprouts

This study aimed to evaluate the response of Triticum aestivum to hydrogen water (HW) and trace elements treated with HW. A pot experiment was conducted to assess the growth indices, secondary metabolites, and antioxidant levels. The response surface methodology (RSM) approach was used to ascertain the concentrations and significant interaction between treatments. The outcomes demonstrated that the combined treatment of Se acid and Mo oxide exhibited a notable positive effect on the growth and secondary metabolites, when treated with HW as compared to distilled water (DW). Notably, the interaction between these two treatments is significant, and the higher response was observed at the optimal concentration of 0.000005% for Se acid and 0.06% for Mo oxide. Additionally, an in vitro experiment revealed that the mixture treatment inhibits the accumulation of lipids in HepG2 hepatocytes cells. Moreover, metabolic analysis revealed that upregulated metabolites are linked to the inhibition of lipid accumulation. In addition, the analysis emphasizes that the continued benefits of higher plants as a renewable supply for chemicals compounds, especially therapeutic agents, are being expanded and amplified by these state-of-the-art technologies.

Evolutionary studies of the bHLH transcription factors belonging to MBW complex: their role in seed development

BACKGROUND AND AIMS

The MBW complex consist of proteins belonging to three major families (MYB, bHLH and WDR) involved in various processes throughout plant development: epidermal cell development, mucilage secretory cells and flavonoid biosynthesis. Recently, it has been reported that TT8, encoding a bHLH transcription factor, is involved in the biosynthesis of flavonoids in the seed coat and it also plays a role in bypassing the postzygotic barrier resulting from an unbalance in genetic loads of the parental lines. Here, we focus on the functional evolution, in seed development, of the bHLH proteins that are part of the MBW complex, complemented with a literature review.

METHODS

Phylogenetic analyses performed across seed plants and expression analyses in the reproductive tissues of four selected angiosperms (Arabidopsis thaliana, Brassica napus, Capsella rubella and Solanum lycopersicum) allow us to hypothesize on the evolution of its functions.

KEY RESULTS

TT8 expression in the innermost layer of the seed coat is conserved in the selected angiosperms. However, except for Arabidopsis, TT8 is also expressed in ovules, carpels and fruits. The homologues belonging to the sister clade of TT8, EGL3/GL3, involved in trichome development, are expressed in the outermost layer of the seed coat, suggesting potential roles in mucilage.

CONCLUSIONS

The ancestral function of these genes appears to be flavonoid biosynthesis, and the conservation of TT8 expression patterns in the innermost layer of the seed coat in angiosperms suggests that their function in postzygotic barriers might also be conserved. Moreover, the literature review and the results of the present study suggest a sophisticated association, linking the mechanisms of action of these genes to the cross-communication activity between the different tissues of the seed. Thus, it provides avenues to study the mechanisms of action of TT8 in the postzygotic triploid block, which is crucial because it impacts seed development in unbalanced crosses.

Insight to phytochemical investigation and anti-hyperlipidemic effects of Eucalyptus camaldulensis leaf extract using in vitro, in vivo and in silico approach

Hyperlipidemia is a key risk factor mainly for hypertension and cardiac abnormalities. Previously eucalyptus plant (river red gum) had been used for its medicinal value for the treatment of many ailments. This study focused on phytochemical examination, investigation of an in vitro potential and in vivo effects in mice fed with high cholesterol diet, GC-MS analysis of extracts of Eucalyptus camaldulensis leaves and further confirmation of anti-hyperlipidemic potential of different constituents of plant extracts by using in silico technique. For in vitro study screening of different extracts of Eucalyptus camaldulensis leaves was performed by using pancreatic lipase enzyme inhibition assay. Ethanolic extract presented the highest potential among all the extracts by inhibiting pancreatic lipase having IC50-11.88 µg/mL. For in vivo study mice were fed with high cholesterol diet for induction of Hyperlipidemia. Water extract showed great anti-hyperlipidemic potential by reducing the level of cholesterol, triglycerides, low density lipoproteins and increasing high density lipoproteins level significantly (p < 0.05). Moreover, molecular docking and prime MM-GBSA study were applied for screening of compounds having anti-hyperlipidemic potential which showed that Alpha-cadinol was the lead compound for inhibition of pancreatic lipase enzyme having docking score (-6.604). The ADMET properties and toxicity profile of the top docked compounds were also detailed for ensuring their safety aspects. In this way in silico analysis substantiate the experimental findings by showing anti-hyperlipidemic potential in constituents of eucalyptus plant. Thus, there is a need of advanced research for isolation of active constituents having said anti-hyperlipidemic potential in the Eucalyptus camaldulensis plant.Communicated by Ramaswamy H. Sarma.

Plants and endophytes interaction: a "secret wedlock" for sustainable biosynthesis of pharmaceutically important secondary metabolites

Many plants possess immense pharmacological properties because of the presence of various therapeutic bioactive secondary metabolites that are of great importance in many pharmaceutical industries. Therefore, to strike a balance between meeting industry demands and conserving natural habitats, medicinal plants are being cultivated on a large scale. However, to enhance the yield and simultaneously manage the various pest infestations, agrochemicals are being routinely used that have a detrimental impact on the whole ecosystem, ranging from biodiversity loss to water pollution, soil degradation, nutrient imbalance and enormous health hazards to both consumers and agricultural workers. To address the challenges, biological eco-friendly alternatives are being looked upon with high hopes where endophytes pitch in as key players due to their tight association with the host plants. The intricate interplay between plants and endophytic microorganisms has emerged as a captivating subject of scientific investigation, with profound implications for the sustainable biosynthesis of pharmaceutically important secondary metabolites. This review delves into the hidden world of the "secret wedlock" between plants and endophytes, elucidating their multifaceted interactions that underpin the synthesis of bioactive compounds with medicinal significance in their plant hosts. Here, we briefly review endophytic diversity association with medicinal plants and highlight the potential role of core endomicrobiome. We also propose that successful implementation of in situ microbiome manipulation through high-end techniques can pave the way towards a more sustainable and pharmaceutically enriched future.

Flavonoid production in tomato mediates both direct and indirect plant defences against whiteflies in tritrophic interactions

BACKGROUND

The role of plant flavonoids in direct defences against chewing and sap-sucking herbivorous insects has been extensively characterized. However, little is known about flavonoid-mediated tritrophic interactions between plants, herbivorous insects and natural enemies. In this study, we investigated how flavonoids modulate plant-insect interactions in a tritrophic system involving near-isogenic lines (NILs) of cultivated tomato (Solanum lycopersicum) with high (line NIL-purple hypocotyl [PH]) and low (line NIL-green hypocotyl [GH]) flavonoid levels, with a generalist herbivore whitefly (Bemisia tabaci) and its predatory bug (Orius sauteri).

RESULTS

By contrasting levels of tomato flavonoids (direct defence) while manipulating the presence of predators (indirect defence), we found that high production of flavonoids in tomato was associated with a higher inducibility of direct defences and a stronger plant resistance to whitefly infestation and stimulated the emissions of induced volatile organic compounds, thereby increasing the attractiveness of B. tabaci-infested plants to the predator O. sauteri. Furthermore, suppression of B. tabaci population growth and enhancement of plant growth were mediated directly by the high production of flavonoids and indirectly by the attraction of O. sauteri, and the combined effects were larger than each effect individually.

CONCLUSION

Our results show that high flavonoid production in tomato enhances herbivore-induced direct and indirect defences to better defend against herbivores in tritrophic interactions. Thus, the development of transgenic plants may present an opportunity to utilize the beneficial role of flavonoids in integrated pest management, while simultaneously maintaining or improving resistance against other pests and pathogens. © 2023 Society of Chemical Industry.

Molecular mechanism overview of metabolite biosynthesis in medicinal plants

Medicinal plants are essential and rich resources for plant-based medicines and new drugs. Increasing attentions are paid to the secondary metabolites of medicinal plants due to their unique biological activity, pharmacological action, and high utilization value. However, the development of medicinal plants is constrained by limited natural resources and an unclear understanding of the mechanisms underlying active medicinal ingredients, thereby rendering the utilization and exploration of secondary metabolites more challenging. Besides, with the advancement of research on biosynthesis and molecular metabolism of natural products from medicinal plants, the methods for studying the biological activity and pharmacological effects of these products are constantly evolving. In recent years, significant progress has been made in the biosynthetic pathways and related regulatory genes of secondary metabolites in medicinal plants, which has greatly advanced both basic research and the development of clinical applications for medicinal plants. In this review, we discuss the past two decades of international research on the development of medicinal plant resources, mainly focusing on the biosynthetic pathway of secondary metabolites, intracellular signal transduction processes, multi-omics applications, and the application of gene editing technology in related research progress. We also discuss future development trends to promote the deep mining and development of natural products from medicinal plants, providing a useful reference.

Antimicrobial to anti-herbivore: Sakuranetin in rice efficiently inhibits brown planthopper by targeting their beneficial endosymbionts

In rice, biosynthesis of specialized metabolites active against insect herbivores is elusive. The major known defense metabolites in rice against the destructive phloem-sucking herbivore brown planthoppers (BPH) (Nilaparvata lugens) are proteinase inhibitors, phenolamides and some terpenes (Xiao et al., 2012), which are induced during the invasion. Specifically, phenolamides were found to be induced upon herbivory with different feeding guild, including chewing and phloem-sucking, but could only provide defense against phloem-sucking BPH, though the clear mode of action of phenolamides has not been explored yet. Moreover, the jasmonic acid-mediated modulation of biosynthesis of these specialized metabolites in rice is not elucidated yet. However, a recent study by Liu et al. (2023) demonstrated that sakuranetin, a phytoalexin in rice, was induced upon BPH invasion and showed significant detrimental effect on herbivore's performance by targeting their beneficial endosymbionts. This is the first report on a strong bioactive anti-herbivore molecule observed in rice with an unusual mode of action. In this article, a view has been presented on this work, its impact and exceptionality.

Heterologous expression of PtAAS1 reveals the metabolic potential of the common plant metabolite phenylacetaldehyde for auxin synthesis in planta

Aromatic aldehydes and amines are common plant metabolites involved in several specialized metabolite biosynthesis pathways. Recently, we showed that the aromatic aldehyde synthase PtAAS1 and the aromatic amino acid decarboxylase PtAADC1 contribute to the herbivory-induced formation of volatile 2-phenylethanol and its glucoside 2-phenylethyl-β-D-glucopyranoside in Populus trichocarpa. To unravel alternative metabolic fates of phenylacetaldehyde and 2-phenylethylamine beyond alcohol and alcohol glucoside formation, we heterologously expressed PtAAS1 and PtAADC1 in Nicotiana benthamiana and analyzed plant extracts using untargeted LC-qTOF-MS and targeted LC-MS/MS analysis. While the metabolomes of PtAADC1-expressing plants did not significantly differ from those of control plants, expression of PtAAS1 resulted in the accumulation of phenylacetic acid (PAA) and PAA-amino acid conjugates, identified as PAA-aspartate and PAA-glutamate. Herbivory-damaged poplar leaves revealed significantly induced accumulation of PAA-Asp, while levels of PAA remained unaltered upon herbivory. Transcriptome analysis showed that members of auxin-amido synthetase GH3 genes involved in the conjugation of auxins with amino acids were significantly upregulated upon herbivory in P. trichocarpa leaves. Overall, our data indicates that phenylacetaldehyde generated by poplar PtAAS1 serves as a hub metabolite linking the biosynthesis of volatile, non-volatile herbivory-induced specialized metabolites, and phytohormones, suggesting that plant growth and defense can be balanced on a metabolic level.